[gmx-users] Problem regarding Complex ion addition by genbox
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Mon Jan 28 10:15:50 CET 2008
> Thanks for giving me insight. But i have a query.
> I tried to add complex ion by genion but while adding, it replaces the
> water molecule according to my choice but it shows information of one atom
> only not of all atom of that complex molecule in structure file (.gro).i
> then tried to use by genbox.How should it will display information of all
> atom of complex molecule ?
I'll do my best to answer, but if you want some better help then I am
afraid that you need to find somebody on your end that can assist you
in getting the question across in english that is more easily
understood. Unfortunately I do not understand your particular question
on this post, I only assume that you still don't have the answer.
Here is what I would first think of doing (but I have never tried it).
1. Use editconf to put your protein in the box of desired size (protein.gro).
2. Use editconf to put your guanidinium ion in a box of such a size so
that it is at the desired concentration (guanidinium.gro).
3. genbox -cp protein.gro -cs guanidinium.gro -o protein_guanidinium.gro
4. grnbox -cp protein_guanidinium.gro -cs tip3p.gro -o
6. Posre ME
Hope it helps,
>> I tried with genbox option with perticular concentration i.e.
>> number of each component like guanidium ion thiocynate ion & water
>> molecule.But while doing PR(position restrain MD) it showing errors :
>> constraints errors in algorithm shake at step 0. t=o.oo ps : water
>> molecule starting at atom 3010 can not be settled. check for bad
>> and/or reduce the time steps.
> Quote from 'genion -h',
> "For larger ions, e.g. sulfate we recommended to use genbox."
> If you must use genion for some reason then the only question I see is:
> Did you do EM? If not then try that first. Also, for genion or genbox,
> you might try simplifying your system. Take a box of water and use
> genion to add a single guanidium. Then EM, then MD (dt=0.002). What
>> i reduced the time steps in pr.mdp from .002 to .001 ps file but again
>> shows the same problem. i have seen the pdb files after genbox really
>> close contacts between was there it means insertion of extra molecule by
>> gen box is not proper it leads to some bad contacts.
>> The real problem is that when performing simulation of peptide with
>> guanidium ion , CL- , water it is showing no problem because CL- is
>> in genion steps. Only change in new system (guanidium ion, SCN- , water,
>> peptide) is of SCN-. Addition of SCN- in genbox step is creating
>> Is any other method to perform simulation of peptide in solvent systrm
>> (guanidium ion, SCN-, water).
>> Please give me some insight to resolve this issue.
>> This is pr.mdp file
>> title = Nanomer ; a string
>> cpp = /lib/cpp ; c-preprocessor
>> define = -DPOSRES
>> dt = 0.001 ; time step
>> integrator = md
>> tinit = 0.0
>> nsteps = 100000 ; number of steps
>> nstcomm = 1 ; reset c.o.m. motion
>> nstxout = 500 ; write coords
>> nstvout = 500 ; write velocities
>> nstfout = 0
>> nstlog = 500 ; print to logfile
>> nstenergy = 500 ; print energies
>> nstlist = 10 ; update pairlist
>> ; Neighbour Searching
>> ns_type = grid ; pairlist method
>> ; Electrostatics and VdW
>> coulombtype = PME
>> vdwtype = shift
>> rlist = 1.5 ; cut-off for ns
>> rvdw_switch = 0.8
>> rvdw = 1.4 ; cut-off for vdw
>> rcoulomb_switch = 0.8
>> rcoulomb = 1.5 ; cut-off for coulomb
>> ;Temperature coupling
>> Tcoupl = berendsen ; temperature bath
>> ref_t = 298 298
>> tc-grps = Protein Non-Protein
>> tau_t = 0.1 0.1
>> ; Pressure coupling
>> Pcoupl = no ; pressure bath
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Velocity generation
>> gen_vel = yes ; generate initial
>> gen_temp = 298.0 ; initial temperature
>> gen_seed = 173529 ; random seed
>> constraints = all-bonds
>> constraint_algorithm = shake
>> shake_tol = 0.0001
>> kinshuk at chem.iitb.ac.in wrote:
>>> Hi all,
>>> I have been trying to simulate peptide in water box with guanidium
>>> thiocynate ion(SCN-).I tried to add these ion by genion command line by
>>> simply adding topology information of these ion in ions.itp of gromacs
>>> library directory but it is not working properly it only adds one atom
>>> by replacing water molecule it seems that genion is applicable only for
>>> monoatomic ion.
>>> If i have to do simulation with these polyatomic ions with perticular
>>> salt concentration how do i will perform it.
>> with genbox. compute number yourself.
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